Frequency analysis of the electrocardiographic RR interval is a common method of quantifying autonomic outflow by measuring the beat-to-beat modulation of the heart (heart rate variability; HRV). This review identifies a series of problems with the methods of doing so – the interpretation of low-frequency spectral power, the multiple use of equivalent normalised low frequency (LFnu), high frequency (HFnu) and ratio (LF/HF) terms, and the lack of control over extraneous variables, and reviews research in the calendar year 2012 to determine their prevalence. Results support the mathematical equivalency of ratio units across studies, a reliance on those variables to explain autonomic outflow, and insufficient control of critical experimental variables. Research measurement of HRV has a substantial need for general methodological improvement.